I'd love to cruise from San Juan. My last cruise left from New Jersey...PR
gets you to the warm much faster, also lets you get much further into the caribbean.
While it wouldn't bother me at all, you'll find that many of the passengers are from Puerto Rico and speak Spanish. Check your dates carefully, they sometime have groups celebrating quinceaneras, and can be mobbed with teenagers.
Cruises from San Juan usually leave port late at night, so you essentially have another full day on the island, but you can board the ship around mid day.The airfare to San Juan can also be quite pricey when added to the cruise cost.
Otherwise, it sounds like a great choice.
hope you will come back and let us know what you decided and which ship.