Puerto Vallarta to San Blas
Most people fly into Puerto Vallarta.  There are 4 buses daily from Puerto Vallarta to San Blas (7am, 10am, 12 noon and 3pm - subject to change).* The trip to San Blas takes 3 1/2 hours. There are no bathrooms on these buses - nor do they make stops. The bus station is located about a mile from the airport.  (The buses from PV to San Blas are running again after 2 bridges collapsed this summer). Another option is to take a bus to Las Varas and a taxi from there.
To save money on the taxi, go out of the airport and walk over the bridge across the street before taking the taxi. (A taxi from here costs $12 to town, to the bus station much less, maybe $4).   You can hire a taxi from Puerto Vallarta to San Blas for about $120 dollars. By the way, if you get hungry there is a very good place for marlin burritos over the bridge from the airport. If you have to spend the night in Vallarta, the Aztec Hotel on Calle Madero is good - about $35 a night for a double and there are many good cheap restaurants in that area. There is an hours time difference between San Blas and Puerto vallarta - PV is one hour later than San Blas. This is very inportant to know for your return trip.
*Buses from San Blas to Puerto Vallarta leave at 7:30, 10, 1:30 and 4:30.

By Bus
You can take a bus from Tijuana for about $50 to $90USD.  It takes 33 hours (although they will always tell you it is 24!).  Except for the movies, the trip is not bad because they stop a lot for food and exercise.  Buy a ticket for Tepic, but ask the bus driver to let you off at the 'crucero de San Blas' and catch another bus into town.  Last bus at the crossroads goes by around 7:30 in the evening.

San Diego Border Information
If you are going by bus, or flying from Tijuana, this info might be helpful. On the American side in San Ysidro, there is a trolley right accross the border that can take you downtown - there is a shuttle bus from the trolly to the airport from Santa Fe Depot (train station) downtown. The trolley runs about every 15 minutes from early morning to late at night. Going into Mexico you first enter a no mans land - right after you go through the gates there is a place to get a tourist visa on the left.

Mazatlan to San Blas
They do not have a direct bus from Mazatlan to San Blas anymore. You should take the bus to Tepic and get off at the 'crusero de San Blas'. Trip takes about 5 hours. Last bus at the crusero runs around 7:30PM.

Guadalajara to San Blas
Take a bus to Tepic (3 hours), then change in Tepic for San Blas (2 hours). It is best to take the express bus to Tepic - the one that goes through Ixlan takes quite a bit longer. (The last bus from Tepic to San Blas runs about 7:30PM).