The 6400 can turbo to 3ghz on all 4 cores - it is ever so slightly weaker than the 4460 on paper.
In real life you could stick the 2 side by side & not see a difference.
Both good cpu:'s , the 6400 is on the latest socket so theoretically would be the better choice for upgradability
However both will last you 4-5 years easily IMO so go for what fits your budget best. Socket 1150 boards & DDR 3 ram are cheaper than skylake boards & ddr4 so its budget dependant.