Is it better to use a visa run agency or take the Green Bus for a border bounce from Chiang Mai to Mae Sai?

Green bus, far more comfortable and safer than a van. Book at least a week in advance for a VIP seat (they do sell out). It is a long day, if you're not up for ~12 hours break the trip and overnight in Mae Sai. Cheap hotels, reasonable sort of market and food. Tachilek itself is only slightly more favorable than cancer but if you want to do something different visit the casino (about a 15 min ride) it makes for a good drinking story :)

Another vote for green bus. Book VIP seat online and pay at 7-11. Give yourself 2 hours to deal with the border and grab something to eat.

It's easy enough to do with the Green Bus yourself and you shouldn't need a tour agency. It's a pretty long day though (4-5 hrs each way, IIRC, leaving yourself a couple of hours to do the visa stuff and have a stroll around Tachilek if you want).

Get the green bus early in the morning .when u arrive in Mae sai there's a songtaew waiting to take you to the border .easy.....