Are the crowds always bad at Vatican City or is there a certain time of the year (or a certain time of day) when things slow down a little? I have a feeling the answer is going to be “Nope, they’re always crowded,” but figured I’d ask just in case!
Like the ancient monuments in Rome it’s best to book ahead for visits to the Vatican City if you want to go into the Basilica, the Sistine Chapel etc. Best times of year are between the end of November and mid-February when the weather is colder. Avoiding the obvious (Christmas). As for the best time of day. Mornings are worse. Afternoons are slightly better. If you are there in the warmer weather go late at night or (for taking photos) very early in the morning.
The crowds are obviously particularly present during the summer. I highly recommend to book in advance, as @Chantal said, for the Vatican Museums. Being the Basilica a church, you cannot really book an entrance, unless you are on a guided tour, I guess. The queues for the basilica are present, just because of the security checks that take place in front of it, in between the columns of Bernini.
I don’t know if you have instagram, but if you need help to find the website of the Vatican Museums, I filmed a short guide here https://www.instagram.com/fka_sara/
As others have already said, the crowds at the Vatican City are exactly what you’d expect for a major tourist spot. Time of year, time of day and religious festivals are important factors. Book in advance on line and get there an hour before your tour starts.
Try to visit at a time when there’s no school holidays. Because those are the times that families won’t be visiting (as the kids have to be in school).