Either one is good. The rum factory tour is taken from downtown--there is a ferry, then a short taxi ride. Tour is very interesting and samples are good! You can do this on your own. The rainforest will involve more walking and will be at least an hour busride away. It is beautiful, tho.
Rainforest will probably take a good chunk of the day. Rum factory can be done on your own, then you can do other things in San Juan.
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