I would first research, see how much of a market there would be as it would be costly to do and since squirrels aren't legal as pets in many states, might not be enough owners.
I would write to someone who does it?
http://www.fufufashions.com/
Order something and then find a local friend/whomever to help you sketch/design/sew a few things based on looking at how the pieces you ordered "work", put up a Web site and have at it.
Get a pet catalog
http://www.gwlittle.com/cat/Clothing...FQ2aOAodJis_WA find out how they measure the pet, etc.
See if this board has any suggestions:
http://thesquirrelboard.com/forums/index.php
Patents are around $1,000 but I don't know that you could patent "clothes" -- nothing wholly unique there, no "idea". You can't patent "gloves" -- doesn't matter if they're for people or squirrels. Look at the "knockoffs" of designer items; they're perfectly legal only the name is copyrighted.