Generally, yes, magistrate internships are less "prestigious." But if you are at all a decent salesman / advocate for yourself, you should be able to have a ton to speak about during 2L interviews. Interning with a mag will get you a lot more experience that firms care about for young associates than interning for a district judge. You will be handling discovery disputes, procedural motions, and other "nuts and bolts of litigation" stuff on the fly. This stuff comes up in every case, so your experience will translate to any case you may be staffed on in the future. You'll be able to talk about this in interviews and the attorneys will be impressed with this type of experience instead of the typical "well, interning with district judge ____, I wrote a memorandum opinion on [insert discreet area of random law here]."
Also, the above poster is correct - take the time to network and get to know all the other judges and law clerks.