Question: things to do in san juan on a rainy day?
Answer: El Yunque Rainforest. Provided the weather is not too horrible, then why not head on over to El Yunque; after all it's named a rainforest for a reason. ... 
Jump in the Car. ... 
Take a snorkel / scuba / kayak trip. ... 
Take an Adventure Tour. ... 
Sector Sixty6. ... 
Visit a Museum. ... 
Shopping. ... 
Catch a Movie.