Both are good we can't compare each other. A deemed university by itself is always autonomous, but it may not be vice versa.

To explain, a university is called "deemed", if it been granted the status, by act of a parliament, to be considered EQUIVALENT to any UGC funded university. This deemed university will conduct it's own examinations and would award degrees of its own. While, this is not the case with an autonomous colleges. Any autonomous college only has the privilege to hold it's own examination and cannot award degrees, which is the sole right of it's parent or the university it has been affiliated with.

Both exercise independent control over its day to day operations and curriculum.