What I usually do is put a servo arm on the choke shaft, and then a short length of pushrod connected with a ball link. This then goes through the cowl and is accessible from outside with the cowl on. I use a small rubber grommet in the cowl for where the pushrod passes through. Sometimes it is a hassle to feed the pushrod through the cowl when installing the cowl, but it works. Another method is a choke servo, as mentioned.
Yet another idea would be to arrange a mechanism that would allow a choke pushrod to be accessed through the front cowl opening.
AV8TOR