St Peter's and Vatican Museum later in the day

The most frequently mentioned issue with St. Peter's is the length of the security line, not crowding inside, though I assume there are always many people there. In my experience in other churches (haven't been to St. Peter's recently), crowding isn't as big a problem as at other types of sights because so much of what you're looking at in churches is above people's heads. YMMV.

New this year is the ability to book an entry time and audio guide for St. Peter's; that gets you into a much shorter security line and is clearly the smart way to go. St. Peter's opens at 7 AM, I think, so if you are an early riser, that might be an option. I looked at the security line at about 4 PM one day in March 2024 (when online booking wasn't an option) and left immediately because the line was so long. (Reports are that the line does move fast.)

Some visitors have felt the Museums were somewhat less crowded later in the day, but they are huge. How sure are you of how much time you'll want to spend inside? It would be a shame to show up 3 hours before closing (for example) and not have time to see everything of interest. Whatever time you choose, be sure to pre-book entry well in advance; online entries do sell out ahead of time (sometimes way ahead of time), and you do not want to be stuck in the (outdoor) ticket-buying line. Even with prebooking, there may be a bit of a delay getting in the door, and then you must queue up at ticket counters to convert your entry booking into a physical ticket.

We visited the Vatican Museum and the Basilica in January 2024 and I managed to get a tour that started at opening time. I highly recommend this. There were still a lot of people, but we were ahead of the massive crowds and we could see things without struggle. When we got to the Sistine Chapel there was room to walk around and plenty of seats available. So I got to sit and marvel. It was truly awe inspiring. The Basilica wasn't crowded.

My husband doesn't like to get up early and slept in at the hotel. I got back and told him he has to go, it was too wonderful to miss. I could only get a tour at 1:00 pm the next day, as of course by that time they were all booked up for the morning slots. It was incredibly crowded. The Sistine Chapel was standing room only and no seats were available. It was still worth going, but he didn't have the experience that I had the day before when it was much less crowded in the morning. The Basilica was more crowded than the day before, but not bad.

I have heard that if you visit closer to closing time, it will not be as crowded, but I can only relate my own experiences. Good luck with whatever you decide to do!