My first thought is using MIDI. Also,
Mission made a pedal (I use one) that has a wah-type toe switch. Control one device, and when you want to switch over, click the switch. I think it is called the SP-2.
Thru Tone makes an expensive exp pedal called the
EXP-ULT built into an Ernie Ball pedal, which uses their 'kick switch' to switch between devices, too (look at the bottom of that web page).