I created a Amazon AWS EC2 instance under my account and made an website/ftp on it, now a new partner wants to move the instance under his company account so his company can pay
The short answer is: No, you cannot move an running instance from one account to another unless and ofcourse AWS Technical support has some magic available behind the curtains.
You can However, Create an AMI from this instance and share this AMI with other users/account. refer: http://aws.amazon.com/articles/530