I think it's been hinted a few times in Batman: The Animated Series and its sequel The New Batman Adventures. As far as I can remember, it's been hinted twice:
Batman: The Animated Series Episode 56: Harley and Ivy:
When the Joker fires Harley, she tries going on a crime spree of her own, joining up with Poison Ivy, and the two become Gotham's Queens of Crime, much to the Joker's fury.
Harley spends the night at Ivy's, and in the morning there is a scene of the two preparing breakfast. Notice the clothing:
The New Batman Adventures Episode 1: Holiday Knights:
Poison Ivy and Harley Quinn kidnap Bruce Wayne and use his credit cards for a shopping spree.
Prior to kidnapping Bruce, there's a scene of the two in their hotel room. Notice the clothing and that there's only one bed:
I think (as I haven't seen all the DCAU) that that's the closest they got at hinting it. Keep in mind that it's the DCAU.