When something uses your total level, it says so
The rules on Multiclassing include the following:
The experience point cost to gain a level is always based on your total character level, as shown in the Character Advancement table, not your level in a particular class. [...]
Your proficiency bonus is always based on your total character level, not your level in a particular class. [...]
A piece of the PHB errata to this section states:
If a cantrip of yours increases in power at higher levels, the increase is based on your character level, not your level in a particular class.
All of these cases explicitly use your total level and not your levels in a class. Lacking a similar exception for the Control Undead feature, we conclude that it uses your class level and not your total level.
Furthermore, multiclassing is an optional rule so it makes sense that the rules weren't written to account for characters with multiple classes. This would explain why proficiency bonus, cantrip scaling, and experience points needed to be called out explicitly and why Control Undead would be about your paladin level.