I'm not aware of any index for the comparison of autonomy within EU regions. There are studies such as Europe's Working Regional Autonomies - A Comparative Analysis by Thomas Benedikter. See also The working autonomies in Europe and The World's Working Regional Autonomies.
Notice that there is a difference between Regionalism (see also Unitary States) and Federalism. I don't think it would be fair to compare Germany (a federation much like the European Union) to a Unitary State such as Spain (and by consequence its administrative regions). In fact you'll probably never see the German regions ever being considered in any list of autonomous administrations.
That being said Benedikter has used criteria such as legislative, financial, executive powers, political representation among others to make the comparison. The Spanish communities are indeed very autonomous by European standards (and likely by World). They are not, however, the regions with highest level of autonomy. Quoting Benedikter:
Considering the whole range of these ten autonomy systems in Europe
under the above listed criteria it is possible to form a first ranking
focusing on the real depth and extent of self-governance. Of course
this evaluation scheme is a very rough and provisional, but it should
just help us to understand that, due to political, historical and
social background, autonomy systems have developed differently and are
a flexible means to solve different problems.
The Ålands Islands detain the most complete and far reaching autonomy.
Under the Act of Self-Government of 1991 the Ålanders enjoy
legislative and executive powers in nearly all political sectors which
matter for the peoples on the islands.
As for the specific case of Spanish regions:
Also the Spanish autonomous communities, and in particular the
autonomy systems of the historical "nationalities" of the Basques, the
Catalonians and the Galicians, can be qualified as comprehensive
autonomies with legislative and executive powers in nearly all
internally relevant political affairs and a government which is
responsible only to the regional autonomous parliament. They have not
only budgetary autonomy, but clear-cut powers of taxation, shared with
the central state. Spain's autonomous communities have their own civil
and administrative judiciary, but the Basque Country and Catalonia
have even their own police force. The Spanish autonomous communities
are also vested with a competence normally reserved only to federated
member states of a federalist union, the power to elaborate their own
autonomy statutes. The amount of autonomous powers of a region in
Spain is in a high degree up to the region itself which, within the
constitutional framework, can freely regulate its own autonomy. Hence,
Spain's regional autonomies are continuously extended and improved.
However the autonomy statutes have to be approved with simple majority
by the central parliament of Madrid.
So your quote:
... the Autonomous communities have the highest level of autonomy among
the European Union
Is perhaps an exaggeration but not far from the truth. Also notice that there are differences in between different regions of Spain.