Any Ideas on afordable after maker ECU for gen 3 sw20 3sgte

Depends how much you want to spend, if you want to re wire the engine with new sensors, triggers, outputs ect or plug and play or adapter loom, if it needs to look factory ect, who will be tuning it? ask them what ECUs they work with.
 
The Vipec 'Plug In' replacement board MR2 is a great choice.

Depends on your definition of affordable I guess!
 
The DIY style megasquirt is probably one of the cheapest ECU's out there. http://www.megasquirt.info/
 
Otherwise, we've got an Apex'i Power FC for 3SGTE $749 (or $825 with commander) http://www.flickr.com/photos/45332128@N07/sets/72157632691837895/ 
Its a tried and trusted swap in ECU that a lot of people have used to get over 300rwkw. Doesn't have all the bells and whilstles that the new ECUs have these days but definitely more affordable, and every tuner knows how to tune it.

MAP ECU 3
http://www.mr2australia.com/mr2play/tm.aspx?m=52149

For Gen3, Power FC for sure. I've run this for years, trusty unit.
 
If going hardcore with flex sensor etc, then Haltech.