I have both they are fine easy prefer MIA more seamless.

Miami is at lot easier and cheaper to get to (you usually have to fly through Miami to get to San Juan). With the plane change and extra flight time, you'll likely have an extra 3-4 hours of travel time on two separate days.

San Juan has some plusses, though. The Old San Juan forts are a lot of fun to tour, plus it will be warmer (you're further south). You'll also see more interesting ports on your cruise as you're starting out closer to the Southern Caribbean. While the airfare will be more expensive, the cruise will generally be cheaper than out of Miami. If you do cruise from San Juan, the Caribe Hilton is great place to stay. You can often get cheap rooms there via Priceline. (See biddingfortravel.com for bidding advice. Have saved hundreds a night using this method).

Enjoy!

How do you disembark? Will you drive off, need a taxi, a shuttle? We didn't have an issues in Miami with a shuttle to FLL.

Thanks triathlete, I know that you usually have to fly through Miami to get to Puerto Rico, but I was able to get a direct flight from Chicago to PR. Also thanks for the info on the Caribe Hilton. We were also looking into the Sheraton in Old San Juan. Any thoughts on that?
Dayenu, we always fly in the day before and stay at a hotel near the port.
The cruise itineraries and prices are very similar, so my biggest question is the ports and the boarding process in each port. In the past I took a cruise that disembarked from New Orleans and boarding was a very easy and pain free process, but I have heard that some ports are a bear to disembark from.

The Sheraton Old San Juan is almost directly across the street from the main cruise pier in San Juan, but you also need to be aware that some cruise lines use another pier that's on the other side of the harbor. Still, the Sheraton is a fine hotel, and if you don't want to stay on the beach, I'd probably choose it over the Caribe Hilton for the proximity to good restaurants and sightseeing before and after the cruise.

I've never embarked or disembarked in San Juan, so I can't tell you if the process is convenient and organized, however. Boarding in Miami is quite easy; it's a very organized ports. Fewer cruises originate in San Juan, but the terminal is busy. Security is a little slow, however.

Disembarkation in SJ has been fine for us twice. Embarkation once was time comsuming d/t a lot of traffic heading to the dock. If you go early like we did the 2nd time it should be better.