Will you rent a car while in San Juan? I'd be tempted to get one for a day trip to El Yunque.
http://www.elyunque.com/about.html
Get an early start and walk the trail to the waterfall, la Mina? before the crowds arrive and take a dip.
Otherise there's plenty to do in and around SJ for 3 or 4 days. The fort was a highlight and we went during the afternoon for an hour or so before dusk. Lovely views and we had the place almost to ourselves (no tour groups at that time of day).

My advice for Vieques? You picked the right place to go. Or the wrong place depending on how you look at it as Vieques is one of those places I hate to leave.
Maybe you could have saved some of the return airfare.

Rent a car asap. I think it's essential and they do run out during busy periods (it will also be expensive). I think we rented from Alan ? last time. He quickly replaced our shiny new car with a beat up old one when the window wouldn't shut. We liked the old beat up one as the roads to some of the more remote beaches aren't perfect.

The beaches are fabulous and the biobay is a magical, out of this world experience.
We took the Island Adventures pontoon twice (not kayak) and I liked swimming under the boat where the total darkness intensified the sparkly dinoflagellates.

It won't be too hard to drag yourselves away from the beaches before sunset (damn bugs!) so you'll be able to enjoy a drink or two on the Malecon before dinner. For casual food we liked Bananas and the view is lovely.

Or you might want to take a horse ride up into the hills and back down to the beach at sunset. My kids did this and loved it.

Tripadvisor has a very active forum if you have any specific questions

thanks very much sassy. I'll start working on the car in vieques. In San Juan we might just get a car for the last three days, with a drop off at the ferry to vieques. I'll consult with trip advisor too, but fodorites are family.

SM,
Here's a link to my old trip report
http://www.tripadvisor.com/ShowTopic-g147326-i649-k2458523-Vieques_Dec_29th_Jan5th_08_report-Isla_de_Vieques_Puerto_Rico.html

The ferry is a fun experience, sometimes! Do get there early if you're travelling on the weekend, during rush hours or on Easter holiday (we did the trip at Thanksgiving once and the lines were very long).

Car for 2/3 days in San Juan would be great especially if you have parking at the apartment.

I miss Vieques! I was reminded of our trips when I put away our Christmas ornaments including 2 handmade glass ones from a small glass art store on the island.

I hope your time there is wonderful and best wishes for retirement.

Thanks for the trip report link. Boy, anticipating and remembering are fun parts of traveling, aren't they? We go to Vieques on a monday and back on a saturday, so maybe lines for the ferry won't be too bad. I'll work on car reservtions for Vieques this weekend.

I reserved a car from Thrifty for several days exploring from San Juan at $30/day and drop off at the ferry in Fajardo with $60 drop off fee, and another car from Maritza for $50/day to get to different beaches in Vieques. I wonder if Vieques will be filled with college kids on Spring Break. Our kids would like that more than we would.

SM, Well done on organising the car hire.

I doubt you'll encounter many spring breakers. Partly because it's not easy/straightforward to get to Vieques and because you really need a rental car to get to the more remote beaches.

Locals tend to prefer Culebra to Vieques for weekends.

Book your Biobay tour too if you know which day you're going. Some slots get booked up by tour operators (you can take a boat trip from the mainland for the biobay and return the same night).

Don't forget your mosquito repellent for the beaches! They don't allow it in the biobay to protect the wildlife. Well the wildlife also bites! I found a small hand held battery fan helped.

Here's an article from wash post about restaurants in san juan

http://m.washingtonpost.com/lifestyle/travel/puerto-rican-food-beyond-rice-and-beans/2013/02/14/3228147c-722d-11e2-ac36-3d8d9dcaa2e2_story.html

See if this helps; It contains some food info from my trip last July:


http://www.fodors.com/community/caribbean-islands/restaurants-in-puerto-rico.cfm