While the other answers are probably sufficient, I want to add my two cents.
Here's what I would do:
- Give them plenty of light
- When the stems get thicker, split them up
Tomatoes, when they're stronger than small seedlings, tend to be fairly tolerant of disturbed roots compared to other plants I've tried, with the possible exception of tomatillos with similarly thicker stems. I mean, you can just pull them like weeds and repot them and they'll be fine. I've done it lots of times. You don't even have to worry about disturbing or breaking the roots. As long as there are still roots on them, they should be fine. They regrow their roots quite quickly. If there are no roots, you can treat them like cuttings, which is somewhat more difficult, but it can work.
However, I must warn you to keep them out of bright sunlight for a day or two after the transplant, because plants with disturbed roots don't do well in bright sunlight. Bright artificial light may also be a problem. This is a bigger problem for cuttings rooted in soil, however, than for tomatoes with any roots at all. (Tomato cuttings rooted in water are probably more light tolerant than those rooted in soil, initially, but I recommend soil.)
Also, if you have damping off problems, when splitting them up you may want to keep as many roots on your tomatoes as possible, since pythium and such probably make breaking the roots a little riskier (but not anywhere as risky as planting a cutting rooted in water into soil with pythium in it would be: there's almost a 100% failure rate there, although maybe bright light would help; not sure about cuttings rooted in soil, because I got soil without pythium in it before I started doing that instead much).
One thing you can do to make this process more gentle on the plants is to soak them in water for a day or two after splitting them up, so they'll grow their roots out a little and heal a bit. This seems more important for peppers than tomatoes. It doesn't seem particularly important for tomatoes, but you can do it. It may increase initial light tolerance, though, but I haven't tested that in particular a lot.
Also, when you transplant them, plant the stem as deep as you can, without putting new growth in the watering zone, and perhaps without having the stem touch the bottom of the container. The plant will be more secure in the pot that way, and it will grow more roots faster (it will grow roots all along the stem). If the only new growth is in the watering zone, the plant will be weaker, grow less quickly, require more light, and might even eventually die without growing out of the watering zone.
While I said to wait until the stems are thicker, you can be successful beforehand. The plants are more tender, then, however, and it's a more delicate process to do without damage to the seedlings. They're also more susceptible to stuff. You'll also want to be a lot more careful with the roots at this point.