For most visitors, it’s easy to walk to all points of interest in central historic Tlaquepaque.
If you’re going further, taxis are plentiful and relatively inexpensive: The 15 minute ride to downtown Guadalajara should cost about $70 pesos ($6 usd).
Local buses are much cheaper still: You can take the Cardinal or the Tur (air-conditioned and less crowded) all the way across the metropolitan area for $12 pesos; and regular buses, which serve many more areas and run more frequently, cost $6 pesos. Information about specific bus routes is available at the tourist kiosks and here. Also, see the "Get Around" section of this website, which provides information about the Guadalajara bus system.
The Tours page provides information about various available tour options in Tlaquepaque.
For longer trips, Mexico’s excellent bus system is available. The deluxe lines tend to be comfortable, clean, and are almost always on time. Most long-distance buses leave from the new bus station (Nueva Central Camionera) near Tonolá, although some (including buses to the Lake Chapala area) depart from Central Camionera Vieja, the old bus station near downtown Guadalajara. Both stations are about ten minutes by taxi or bus from Tlaquepaque Centro.
Car rentals are available at Guadalajara International Airport.