Here's SJ's trip planner service, in a state of perpetual beta
http://www.dtop.gov.pr/mapas/index.asp
And a better bus map, courtesy of Banco Popular
http://www.popular.com/compromiso/pdf/ama/mapas_ama.pdf
If you must take public transit, take the B40 bus to the Isla Verde transfer depot, and from there take the A5 bus straight into San Juan. On the bus, budget 2 hours for this, mostly spent waiting. Explain to the bus driver where you're going, and they should speak enough English to explain to you how to get to where you're going.
Conversely, take a cab or drive and in 15-20 minutes, you'll be there.