SJU is nice. I spent a week driving around the island--a week well-spent, and I'd like to go back. Plenty to do but also plenty of places to relax.

BOS is one of my favorite cities, if only because there is so much history there. I think to really appreciate it, though, you have to enjoy history (although the city has other cultural attractions to offer and, as a college town, can be very lively, if that's what you're looking for).

Some of the cities in the South can be really nice--there are some hidden gems worth visiting. I enjoyed both CHS (for the history, though it can also get very lively at night!) and SAV (a beautiful, historic, peaceful Southern town...with Paula Deen's restaurant right downtown!). If your parents want a relaxing weekend, consider putting them up in a plantation home in Natchez, MS. I stayed a night at the Monmouth Plantation, and I'd have no problem recommending a stay there.

Natchez is in a rural area, so getting there might not be as easy--the closest "major" airport would probably be JAN, which is a 2.5-to-3-hour drive away, although the drive down the Natchez Trace is splendidly beautiful and relaxing as it gently meanders through the countryside, or BTR, about the same distance. You could also consider sending them to Jackson by Amtrak--the total round-trip cost for the two of them in a Superliner Roomette (which would include breakfast, lunch, and dinner, as appropriate) would be (assuming the lowest bucket rooms are available and a 15% senior discount) $518, which is actually less than airfare to JAN, BTR, or even MSY. Rental cars look like they can can be had in JAN (downtown) for about $40 a day (Avis and Enterprise should be able to pick them up at the train station).

Your parents may also enjoy some other rail excursions. I might recommend looking into doing a loop between Chicago and DC involving the Cardinal and the Capitol Limited--there's some spectacular scenery on those routes through the Cumberland Mountains and the Alleghenies (including the spectacular New River Gorge in West Virginia). For a weekend in April, it looks like the total round-trip cost for sleeper accommodations (meals included) would be $764.80, plus a hotel in DC (you can't connect the same day in DC, and besides, they might like to stay there).

Some other options:

• Some of the parts of Central Virginia can be beautiful and relaxing. A stay in the CHO area (also accessible by Amtrak--station code CVS) is very pleasant; while I've only stayed with friends, I imagine there could be some nice, relaxing B&Bs in the area. Plenty to see and do with Monticello, UVa, and the spectacular Shenandoah NP nearby.
• The Brandywine Valley just west of PHL--reminiscent of the area of the same name in Tolkein's Middle Earth. There's a grand, wonderful B&B there called Hamanassett, which was owned at one time by Montgomery Meigs, Lincoln's Quartermaster General. You could spend a week there just recharging your batteries in the peaceful surroundings.
• If you can get a cheap fare to Paris or Lyon, staying in the Burgundy region can be similarly pleasant...and filled with enough culinary memories for a lifetime (if you can, eat at Le Chabrot!). There's a B&B in Dijon I love (Marcs d'Or/new link) as well as one just south in Beaune (Jardins de Loïs); both would make wonderful, relaxing stays and are surprisingly inexpensive.
• If they're into cultural attractions, you can't go wrong with DC.
• San Francisco has tons to offer as well, and if they're looking for something more relaxing than a big city, the wine country has some gorgeous B&B offerings.
• The Atlantic Provinces of Canada are a wonderful hidden gem, too. PEI is rural and relaxing, and Halifax is a lovely and historic town. There's lots of beautiful country in between.