While there are other entries about San Juan markets, it is confusing.    There are 2 main markets(La Placita and Rio Piedras), both some distance from old San Juan.  The biggest is the Rio Piedras market and is the most interesting..  You can taxi, but it's doable via public bus (75 cents; over 60 is 35 cents, correct change only).  A bus can be picked up at the main bus station near Piers 2 and 3 on the edge of Old San Juan.  Information at the bus station is poor, but  take any bus that goes to Sagrado Corazon, which is the nearest connection point to the new Metro train.  Change to the train ($1.50) and get off at the Rio Piedras stop.  The train runs very often and it's only a 10 minute ride from Sagrado Corazon.  The bus to the Sagrado Corazon stop from the main station takes about 15 minutes.  On the way back, your $1.50 train ticket is good on the bus as well.  The train station has automated ticket machines that take credit and debit.

The Rio Piedras Market is a big covered building with lots of fruit vendors and most importantly, 15-20 little mom and pop hot food places in a food court type of setting.  Very authentic and cheaply priced food, so go hungry.  You can also get fruit smoothies that are just wonderful. The area around the market is filled with stores selling very cheap clothes and other everyday items.  It is lively and a slice of real San Juan.