Probably the easiest way to farm the marks alone is to do the sector space Borg Red Alert queues. It populates quickly and generally takes only 3-4 minutes to run one, and it is a decent way to build up Starship Mastery XP as well, even post-nerf when they made this into a regular queue instead of a rotating event. Both this and the Tholian Red Alert will grant a choice of any mark reward pack, so these are good to farm for all other reps as well. However, this only grants marks. If you need the elite Borg marks as well then running ISA is probably the fastest as everyone only runs ISA in space unless there's a new reputation queue. Defera Ground is OK for grinding marks as well but I find it generally takes longer as some of the parts are time-gated with regards to enemy spawns. There are also ground queues which reward Neural Processors but I do not usually bother with these.
As with Omega, there's a sector space queue for a Tholian Red Alert that populates quickly and takes only a few minutes to run, and it allows a choice of any marks. You can also do Crystalline Catastrophe Advanced (CCA) and get Nukara marks in space. I believe the only other place to farm these is on Nukara ground, which is not too terrible in terms of the time investment. Getting a group of 2-3 people for this and running through a full sweep of the missions should only take you 30-60 minutes and net you a significant number of marks. Since Nukara and Romulan reputations do not require elite marks, they have higher regular mark prices, so you'll probably need to spend a lot of time here. The Vault: Ensnared space queue also rewards Nukara marks but is fairly lengthy for the reward gained.
Romulan marks can be gained on New Romulus ground, which I find boring and slow, or on any of the Azure sector space patrols, which is quick. If you can manage 30-40K DPS you can sweep multiple of these sector patrols in 15 minutes or so and gain about 100 marks with the daily bonus. I recommend Japori, Carraya, Acamar; others I have heard are decent but do not run myself are Archer and Galorndon Core. These all involve space combat against multiple waves which are pretty easily dispatched; Acamar has a small text puzzle you can easily figure out as there are only a few "successful" options (opt for the middle ground and choose the "Diplomacy" rank prompt if you have it) which spawn Tal Shiar to fight, or you can piss off the Acamarians and fight them instead for less overall XP and a longer fight. In terms of space queues, you have a few options in shuttles (Vault Shuttle Event or Atmosphere Assault), which I usually only run when there is a bonus event going on for these every few months. There is also Azure Nebula Rescue (time-gated), or The Vault: Ensnared, which are both fairly long for the reward. If you're going for efficiency, just stick to the sector space patrols and do them daily when you log in. They're also good for grinding out the Starship Mastery XP you may need for ship traits.
Dyson marks are most easily achieved by either doing the Dyson Ground Battlezone or the daily in the Dyson Sphere space. The daily usually takes less than 5 minutes to do for the same daily bonus package as anything else which is a good return on time. Ground BZ is the best place to farm the elite marks (Voth Cybernetic Implants); if you join one which is nearly done, hop between instances until you can find another. Right now your only choice for space queues is Storming the Spire, which takes a while. However, there's a regular event called Into the Breach which usually runs once or twice a year where you can get a large number of marks for about 15 minutes of time. If you do need Dyson marks, this is a great time to farm them as you usually get a bonus for running the mission 15 times such as an Admiralty card.
As with Dyson, the Battlezone is the best option here for speedy marks grinding as you can get both regular marks and the elite marks (Isomorphic Injectors) in the same spot. Works best with a team of people though to ensure it gets done in short order. You can also queue for Undine Assault or Viscous Cycle (advanced or higher) for elite marks in space, or Undine Infiltration (advanced or higher) for ground. Of those queues, Undine Infiltration is probably the fastest and easiest to get a group for.
Sector space patrols here will grant the daily marks bonus (if you're only going to do one or two, I recommend Argala and Borg Battlefield for speed). If you need elite marks, doing the two repeatable Kobali ground missions will each grant one elite mark per day (Ancient Power Cells for Delta or Iconian Power Cores for Iconian). These are probably the least time-intensive ways to grind both reps' elite marks. For Delta queues, you can consider Borg Disconnected or Bug Hunt for space and ground, respectively, and on advanced or higher for the elite mark.
As with Delta the easiest farming is on Kobali ground as you get both regular and elite marks. You can also queue for Brotherhood of the Sword (ground) or Gateway to Gre'Thor/The Herald Sphere (space).
Once again, the space Battlezone is the best option for speed and both regular and elite marks. If you do the entire zone you can get both Temporal and Terran elite marks at a decent rate. You can also queue for Counterpoint (space) or Assault on Terok Nor (ground).
Along with the Terran space Battlezone, you can queue for Days of Doom or the Battle of Procyon V (space) or Miner Instabilities (ground) to earn elite marks for the reputation. Miner Instabilities is probably the easiest option here.
The recently added Lukari reputation has a Tzenkethi space Battlezone which is somewhat buggy right now, so I would opt for the space queues instead. Of the two, Gravity Kills takes a lot longer and seems to encounter more potatoes in the pug queues. Go for Tzenkethi Front instead, you can easily do objectives even with bad teammates.