I'm very afraid of plains and I want to take a vaation to Puerto Rico from New York but I want to be able to arrive at P.R and stay for a week or two and then return by ship to N.Y but I don't seem to find any cruise lines that do it that way. Can anybody help me with this?

Trust me it's not going to happen. You are going to have to fly. I hate too fly and looked at doing something similar. But it will be very difficult to pull off. Try though, royal caribbean cruise line that would be the best line to try