The 6 foot 3 inch targetman added to Rowan Vine's eighth minute wonder strike with a powerful header and two neat finishes.
After a bright opening by the Dons, Luton took the lead against the run of play in the eighth minute.
Good work by Paul Underwood down the left found Vine, who picked up the ball 25 yards out, cut inside and unleashed an unstoppable strike into the top corner of the net.
The Dons almost hit back moment later when Wade Small put Izale McLeod through, but his well-struck shot from an acute angle was well-saved by the returning Marlon Beresford in the Luton goal.
Howard thought he'd doubled the visitors' advantage in the 18th minute when his header from Ahmet Brkovic's corner flew into the top corner, but it was ruled out for a push.
Small missed a golden opportunity to equalise for Milton Keynes just before the half-hour mark when McLeod found him in space inside the box, but he dragged his effort badly wide.
Howard then returned the favour at the other end firing straight at Dons keeper David Martin from just nine yards after more good work by Underwood.
A magnificent saving tackle on the goal-line by the Dons' Gareth Edds prevented Vine tapping in Brkovic's cross just before the break, but the Hatters weren't to be denied and Howard doubled Luton's advantage in the 44th minute, tapping in from close range after a goalmouth scramble.
However, there was still time for another twist before the interval, with Small pulling a deserved goal back for the hosts from close range after the Hatters failed to clear Nicholas Rizzo's free-kick.
Luton completed dominated the second half with Kevin Foley and Curtis Davies both going close before Howard bagged his second goal of the game in the 66th minute.
Foley's hanging cross to the back post was headed home by the former Northampton striker, with Martin rooted to the spot.
Howard completed his hat-trick in the 83rd minute to cement the Hatters' place at the top of the table.