They didn't get to the lights nearly fast enough. You need to move to lights - if they aren't already under them, as soon as they break the soil. Now they are leggy so transplant them deeply.

Cover/top - NO. It is for germination only and not really needed even for that. If you put it on now it just leads to damp-off. Check out the FAQ here on How to grow tomatoes from seed.

Better in a window? No, depending on what you have for lights? Close, intense, supplemental light is better right now than a window but it takes a lot of it. Lots of discussions here on light set ups - several with pictures over on the Growing from Seed forum. Check them out.

Dave

Should I go ahead and transplant even though they don't have any true leaves, just the two?

Don't transplant yet wait on more leaves. I can't understand you poor germination rate. I planted about 500 tomatoes & peppers last month with a germination rate of about 99%. I filled my trays up with seedstarting soil, soaked them in water, put the seeds almost on top of the trays, sprinkled a light cover of mix on top, put the covers on them and had full trays in a few days. These are just HD and wal-mart seeds mostly.

He said they germinated within a day. The others will probably come up later. I don't know how you got them to come up in a day?

Sorry I read it wrong. They grew tall in a day. I still think more will come up; they don't all germinate at the same rate.

I explained it wrong - I had them on a heat vent for four days, one moring I looked and they had broken ground and the dame afternoon they were tall.

Moisture and heat without lighting equals very fast growth.

Mike

Mike
I am sure you meant w/o adequate light because that is when the plants grow quickly to reach light if it is too far away and they get lanky

You can still have heat and moisture and lights 12 hrs and off 12 hours and that cooler and dark regime slows growth, and plants get stockier too
Dennis