I don't think it will be a problem. I see people with kids in strollers every year. At times it is very crowded, and maybe someone who has recently gone with a stroller will be able to share their recent experience. My kids are older now, and I have not personally gone with a stroller for about 10 years.
The only problem you might have is if the entrance line is very long, sometimes they wind the queue up and down a flight of stairs in the entryway. Not sure what they do with people who have strollers in that case.
Have fun if you go! Fort Wayne is my hometown. I go every year with my sister and sister-in-law, and we do a girls only shopping trip.
Gretchen