Does EQCompare work without any other addons ? It is over a year old and it is possible that it no longer works with WoW itself. No addon will say it is specifically incompatible with nUI but incompatible with WoW itself.
Also, a comment on the curse page says this :
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For all those with the 'incompatible' error - change your release type to 'beta'. The 'release' version (1.4 something) doesn't work with 3.3. The 'beta' (2.0) does.
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Try the addon and its suggested work around with no other addons around if it still comes up with the message you will need to find an alternative or hope someone will take over the project or come up with an alternative.
EQCompare Link :
http://wow.curse.com/downloads/wow-a...eqcompare.aspx
Edit: Ah, a later comment has a link to this addon:
http://www.wowinterface.com/download...ipCompare.html
Try that one as it sounds like it may be an updated version.