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As with almost all tropical destinations, any time of year is the best time of year to visit San Juan. There are no actual "seasons," in that weather is warm and humid year round, and temperatures can be expected to reach the high 70s and low 80s (Fahrenheit) even in what is technically winter.
The only thing travelers really need to take into consideration when planning a trip to San Juan is hurricane season. In Puerto Rico, hurricane season starts in June and ends in November. It isn’t necessary to avoid visiting during these months - just make sure to remain updated on hurricane warnings and weather reports during the days before your plane departs. Hurricanes never come as a complete surprise, so by staying informed it is possible to have a successful trip even in the middle of storm season.
It does rain pretty much year-round in San Juan, but it’s a warm, tropical rain, so don’t despair at the thought of getting wet. If you really can’t stand precipitation of any temperature, it’s a good idea to plan a visit for mid-February, which is on the dry side. And don’t plan on participating in snowball fights, skiing or making snow angels, because snowfall is almost unheard of even on Puerto Rico’s highest mountain peaks.