RAW: As long as the attack hits another creature, it will return to the thrower's hands.

The text for Dwarven Thrower states the following:

When you hit with a ranged attack using this weapon, it deals an extra 1d8 damage or, if the target is a giant, 2d8 damage. Immediately after the attack, the weapon flies back to your hand.

The usage of the term "immediately" leads me to believe that, for the purposes of the rules, the weapon instantly returns to the thrower's hands. As such there is no time in between the hit and the return of the weapon where its magical properties might be suppressed by the Antimagic Field.

Opinion: Add a skill check to it

The RAW application of this question is rather boring compared to what a player would expect. Intuitively, one might image that the hammer would lose its ability to return to the thrower's hand as soon as it entered the field, consequently falling to the floor or becoming unstable in its flight.

In order to address this, I'd simply require the thrower to make a Dexterity (Acrobatics) skill check to catch the weapon, adding some thematically appropriate penalty if they failed it.