By Vishnu stage 1, do you mean their actual 300 HP stage 1 package? Vishnu considers an ECU reflash only (with no other mods) to be stage 0, unlike Cobb.
Anyway, I went with the Cobb AccessPort. Here's some of my reasons:
1. No downtime. With the Vishnu you have to mail your ECU in and wait for it to come back. With the AccessPort, you do the reprogramming yourself. You're only down for about 10-15 minutes.
2. Price. AccessPort is $595, Vishnu's stage 0 is $650.
3. Flexibility. With the AccessPort I can switch between 91 and 93 octane maps as needed. With the Vishnu you have to pick one or the other and you're stuck with it. Also with the AccessPort, when I decide to go to stage 2 with a turbo back exhaust, it takes a few minutes to reflash my ECU. With the Vishnu, you'd have to send it back in and suffer another few days of downtime as they update the ECU programming. I don't know if Vishnu charges for this upgrade either. With the AccessPort it's free.