I have heard of people waiting for hours to get in the basilica. My husband and I arrived at St. Peter's just before 8am and we got through the line in 10 minutes. At that time of day, the tour groups haven't shown up yet and it's not very crowded. The basilica is absolutely gorgeous, among the most beautiful cathedrals I've seen.
The dome is totally worth it. There are a ton of stairs, the walls are close and there is not a way to turn back if you decide to not go all the way up. If you are not in very good shape or claustrophobic, I would not advise going up to the dome. You first go near the top of the inside of the main dome and see mosaics and the paintings in the dome up close. Then, you walk up others stairs to get to the outside observatory deck where there are fabulous views (and picture taking opportunities) of Rome rooftops and the basilica square.More