Are there boat rides offered from where cruise ships dock in Kotor over to Our Lady of the Rocks Island where the 'Gospa od Skrpjela' church is? If so, does that boat also go to Perast? If anyone has any knowledge regarding if such a boat exists and/or the schedule, I would certainly appreciate hearing from you. Thank you so much!
As a caveat, I have not been on a boat tour from Kotor (only visited the bay on a day trip from Dubrovnik), but I took a quick look on Trip Advisor to see what others have done. Maybe this will give you some ideas:
Last year I took a boat tour from Kotor to Perast that stopped at the church. I'm sorry that I don't remember anything about the schedule. The tourist information booth outside the main gate to the old town will have information, and you'll probably see "Perast" signs on boats along the waterfront. There are buses to Perast also, and there's a good chance you could get to the island from Perast if you go there by bus.
We took the boat from Kotor to our Lady of the Rocks and on to Perast, returning to Kotor. The boat was Ankica and was recommended by the folks who run the Monty B. We walked out of the city walls and there were girls there selling rides on Ankica and one of them walked us over to the boat where we paid for our rides - I don't remember the price, but we thought it pretty inexpensive. About an hour later we turned back up at the boat and sat on the deck up front (about 6 people will fit up front) and maybe around 30 people on the whole boat, and off we went. We had 30 minutes or so at Our Lady of the Rocks, which was plenty, and we then took the option to stay in Perast longer to have lunch. I think our boat stayed for 30 minutes, but we went back on the second boat, so we had 2 hours and 30 minutes. I am sure if you search for Ankica or Miki travel boat tours you can find some exact times, but my recollection is that we left about noon and returned about 4:30. It was a beautiful boat ride.