What is the Membership type 'domain' in the api?
On multisite you tie each membership type to a domain id. You can find what the domain ID's by looking at the civicrm_domain id table (or in the civicrm.setting.php file).

If you create the memberships on the correct domain they will be correct I believe, but if you don't then just adjust the domain_id in the civicrm_membership_type table.

Then only the memberships tied to a certain domain will be available for selection on a given domain.