http://travel.state.gov/travel/cis_pa_tw/pa/pa_3028.html
Most of the worst issues are on the Mexico - Texas border.
It does say, however:
"Robberies, homicides, petty thefts, and carjackings have all increased over the last year across Mexico generally, with notable spikes in Tijuana and northern Baja California. Ciudad Juarez, Tijuana and Nogales are among the cities which have recently experienced public shootouts during daylight hours in shopping centers and other public venues."
I will say right now, if you decide to stay on board you are not missing anything. Of the ports I have been to, it seems like they are all the same:
1) Kids begging for a buck for knockoff chicklets.
2) tourist bars that offer $20 all you can drink so you can get drunk.
3) Crappy goods that were probably made in Taiwan anyhow.
4) Overpriced tequila and all natural vanilla in the touristy areas, where you should stay put at.
5) Oh yeah, the kids from 1) cough all over you, thus the name I gave them: "THE TB KIDS".
If you do decide to go I suggest the following:
1) Group of 4 or more. If at least one of you speaks Spanish, thats a big bonus.
2) Nobody get trashed on Alcohol. If you can walk back to the boat, that is the best condition to be.
3) Stay away from "locals" bars. Furthermore, just stay on the tourists strips.
4) If you dont have to be back on the boat until after dark, just head back to the boat for your dinner before it gets dark.
Have fun,
Matt