I don't have specific figures for Crete. The last Greek census was carried out in 2011. According to that the total population of Greece was 10,815,197 of which 911,929 were permanent foreign residents, i.e. about 8.5 %. Of those 199,101 were citizens of other European countries, i.e. about 2 %. Of the 911,929 the majority were Albanian, 52.7 %, followed by Bulgarian, 8.3 %, Romanian, 5.1 %, Pakistani, 3.7 % and Georgian, 3 %.
The total population of the different Nomos of Crete in that census were:
Crete Total 623,065
If Crete has the same distribution of foreigners as Greece in General, and it may not, then that would suggest a total of around 52,536 foreigners were living here in 2011 of which 11,470 were from other EU countries.
Ref: Greek Reporter Article
With additional information from an Excel spreadsheet