After having central AC install work, I began having the same problem with our boiler for the radiator heat. In our case, it was a loose wire where the thermostat connected at the boiler. It was touching the side and shorting out (which would shut it off just like having a faulty thermocouple).

During this problem I also noticed that the pilot had an orifice on three sides, so I made sure the match was lighting the far side of the pilot.

Not sure if that helps you, but good luck.

I had the exact same problem, and it seemed to be worse in the Winter. Not sure why that was. I was thinking that it was simply the fact that the heater was cycling more often, increasing the chances of a blowout. After trying all the same things you have, I went with the ultimate low tech fix. I cut up a dog food can and fashioned a shield around the pilot. Sounds ridiculous, but it worked. Kept it like that for over a year before finally replacing the heater.

Remove the pilot orifice(you have to remove the entire burner assembly to do this) clean it out really good(an orifice reamer is best). Then with the burner assembly removed clean the burner air inlet and gas ports as well. Then inspect the flue, and reassemble.

Removing burner assembly: turn gas OFF to water heater, remove pilot line from control with a 7/16's wrench, remove T-couple from control with a 3/8's wrench, remove burner supple line from control with a 3/4" or 13/16's wrench(usually reverse threads too), then slide assembly out.
Remove pilot orifice: disconnect pilot tubing from pilot assembly and orifice will fall out usually, sometimes it may be stuck, if so carefully pry it out or clean it in the assembly. If you have no pilot reamers spray some carb. cleaner or contact cleaner into it and immediately blow it out with air.