Yak-9U with a Klimov VK-107A:
*Conservative Figures
575km/h(357mph) @ sea level
672km/h(417mph) @ 5,000m
*Optimistic Figures
600km/h(372mph) @ sea level
700km/h(434mph) @ 5,000m
Yak-3 with a VK-105PF2:
567km/h(352mph) @ sea level
646km/h(401mph) @ 4,100m
The Yak-9U is faster than the Yak-3 both at lower alts and higher alts. It's effectively a lighter, a little bit more maneuverable, at a little lower altitudes version of the Yak-9U. The -9U comes from the "heavy Yak" lineage, and the -3 comes from the "light Yak" lineage.
The 'Yak-3 is the fastest' comments come from performance figures of test bed Yak-3s - about 50 aircraft produced, fitted with VK107A engines. These, never flew in actual combat in WW2.