what is the best website for purchasing tickets to San Clemente?
basilicasanclemente.com
This is really something you don't want to miss!
I purchased two tickets from this website just a couple of days ago. It was very easy to use and I printed the tickets out and also saved a screenshot of the bar code on my phone. The upper church, ground level, is free, but you do have to choose a date and timed entry for the lower levels. There were plenty of times available for dates just a few weeks ahead.
I used that site and was at the church a couple of weeks ago. I had a weird encounter with the attendant in the bookstore in the little annex of the sanctuary when I was trying to go down to the lower levels. That seemed like the obvious place where you present your ticket, but the attendant told us we had to go back into the sanctuary and show our tickets to someone in there. There was no one in the sanctuary other than tourists, so I went to ask the attendant out in the courtyard by the door where you enter. He pointed us back to the bookstore. This time the lady did not say a thing and waved us on towards the stairs. I do not know if she was just messing with us, but for the OP you very much need to go to the bookstore to get to the lower levels.