at 6am, the wait may be an hour.  at 9am, the wait may be up to 3 hours.  Earlier the better!

My guess is you should plan on about an hour, maybe more.  However, if you're on a tight schedule (say you have a flight to catch) then I recommend crossing the night before.

With the exception of Sundays and holidays you can usually cross as a pedestrian in under 15 minutes by waiting until after 7pm.  Hence I recommend afternoon trips and if you finish early I suggest going to one of Tijuana's upscale restaurants for a great meal and cross after dining with a minimal delay.

http://apps.cbp.gov/bwt/

Both Canada and Mexico.

Pedestrian is far right column.
San Ysidro is near the very bottom.

Bear in mind, my info is Old, but should still be valid.  There was/is  a bus that loads near the TJ border that carries mostly Mexican nationals and, at a low rate!  And, it beats the heck out of that long walk into TJ.  The bus goes straight to the main street and makes all the good stops.  As for coming home, again, my experience is very, very, dated.  I can tell you to be very sure you have good ID and lots of it..and, do protect it carefully while in TJ.  It can be very valuable thing for certain types...BTW, that long walk into TJ can be dangerous, or so I have been told...   flyrod