If you want to be close to the port and see your ship come in, I'd suggest the Wyndham in Old San Juan, great views, close to shopping and restaurants in Old San Juan. Its across the street from one of the piers.
Hi Mimi...San Juan is the best! You might find it helpful to read what I wrote on the "Hotels" message board, dated March 1st of '03, under "Some San Juan Suggestions". Wishing you smooth sailing...jeph