You've posted in the Developer forum ... with a question that really isn't for Development. :| Suggest moderater move the posting to some thing more appropriate - like General Help or Upgrading/Migrating forums.
Sorry, but one cannot migrate *and* do a hyperjump upgrade at the same time.
For entire site migration ...
On the destination server, one might need to run lower/compatible version of PHP+PHP extensions/MySQL (if that's the db using), to get the site migrated ... will be same version as you had on old server.
Then map out an upgrade path to 'march' the moodle upwards ...
Use the Server Environment check - update component - then in the drop down pick list for version of Moodle, select each version higher than the 3.3 to see what Moodle says you will need for PHP version+PHP extensions/MySQL versions.
Just after a hop upwards in moodle (not too high), one would need to upgrade the PHP/MySQL to a compatible version that supports your next hop upwards.
See:
http://www.syndrega.ch/blog/#php-and-dbms-compatibility-of-major-moodle-releases
One alternative is to install a fresh 4.1 and get that running, then make backups of courses from the old site (with users/without users) and restore the backups to the new 4.1.
For the latter to work, one needs to see if any addon plugins used in the 3.3 still exist in 4.1 and install those prior to attempting to restore a course that might use those plugins.
Another alternative is to upgrade the old 3.3 in place as high as you can first before migrating to new environment. Migrate the site (here again PHP+PHP extentions/MySQL version important) and then do upgrades to 4.1 on new server.
'SoS', Ken