This question ultimately comes down to definitions. How small a unit is considered relevant? Do you want to know only about the units fighting inside the city itself or about the units fighting in the larger battle of Berlin in general?

The last cohesive unit to surrender within Berlin itself was probably the remnants of LVI Panzer Corps under General Weidling who formally surrendered Berlin in the early hours of May 2nd. There were isolated pockets of resistance that held out a little longer, primarily SS units, foreign volunteers in particular, but none large enough to be considered a cohesive unit of notable size.

In the larger Battle, the last unit I'm aware of were the remnants of the II Army (9th of May in the Vistula delta).

Peter Antill - Berlin 1945