"EEPROM's" because it looks like you're trying for possessive. These terms have no lower case or puncuation, so there is no need for the apostrophe.
The least confusing form is EEPROMs.
But I think that is your own personal confusion since:
CVS's
M.B.A.'s
are both valid - the apostrophe is sometimes used to show plural.
I am not that interested in picking the nit but you tried to insult me in relation to using "'s" to show plural in acronyms - you clearly did not understand that "'s" is sometimes used to show plural. Your attack was bogus, uncalled for, and lacked an understanding of the subject.
I do find it funny that you feel published word definitions need not be followed but published punctuation guidelines must be rigidly followed without any variation or deviation