Select vc.[name], vc.[IsManaged], eulu.[User], eulu.[Last Logon] AS [Last Logon]
from vComputer vc
JOIN inv_aex_eu_logon_users eulu
on vc.guid = eulu._resourceguid
AND UPPER(vc.[User]) = UPPER(eulu.[User])
WHERE eulu.[User] IS NOT NULL
AND eulu.[User] <> ''
GROUP BY vc.Name, eulu.[User], eulu.[Last Logon], vc.IsManaged
HAVING DATEDIFF(DD, max(eulu.[Last Logon]), GETDATE()) > 90
ORDER By max(eulu.[Last Logon]) DESC

not getting the most current LAST LOGON being checked for over 90 days...

I may be wrong, but wouldn't this be gathered by the Exchange inventory, which would be run on a different schedule than say, last logged on user from basic inventory?

references data collected by the Exchange inventory .exe (regular inventory). The basic inventory also collects the logged on user,  and is used to help populate the primary user. This data is collected by basic inventory, which is much more frequent.

Inv_AeX_EU_Logon_Users runs every day I think (I'm not sure; we have completely hacked up the Out-of-box config for Inventory).

yusgab's report will find any machine where the primary user hasn't logged on in > 90 days, but I haven't analyzed it enough to know if it will tell you if ANY user hasn't logged on in that long.  It might also be worth adding the Inv_AeX_AC_Identification.[Client Date] column, which has the current date/time on the system when it last sent basic inventory (which should be every day).  I think this will work:

Select vc.[name], vc.[IsManaged], MAX(eulu.[Last Logon]), acid.[Client Date]
from vComputer vc
JOIN inv_aex_ac_identification acid
on vc.Guid = acid._ResourceGUid
JOIN Inv_AeX_eu_logon_users eulu
on vc.guid = eulu._resourceguid
WHERE eulu.[User] IS NOT NULL
AND eulu.[User] <> ''
AND DATEDIFF(DD, acid.[Client Date], GETDATE()) < 7
AND DATEDIFF(DD, eulu.[Last Logon], GETDATE()) > 90
GROUP BY vc.Name, vc.IsManaged, acid.[Client Date]

ORDER By vc.Name--, max(eulu.[Last Logon]) DESC

If the user inventory is run every day. I don't typically do that, as the logged on user data (from basic inventory) is gathered every day. Always happy to be corrected though.