I agree with banditpony, it will be very subjective and depend on how the custom was made and what character it is.
Leave a Whisper's idea of "if it used a real my little pony as a base then its a my little pony" is pretty compelling! If I paint a rock, it is still a rock. If my sister modifies her Honda, its still a Honda. For selling or other certain purposes it would be critical to point out that the items were modified! But for most everyday conversations, my little pony, rock, and Honda will be sufficient.
BUT! There is also, as BlackCurtains pointed out, the grey area where "my little pony" is used in society like Kleenex is used for a facial tissue (or like Hoover for a vacuum cleaner for Brits!). It is a brand name that has been adapted to a more generic use. If a non-pony collector came over to my house and pointed at a a fakie and said something like "oh I used to have my little ponies as a kid" I don't think I would correct them. I don't personally use the term that generically, BECAUSE I'M A PONY COLLECTOR. Your average person probably couldn't tell the difference between a good fakie (or even a bad fakie) and a Hasbro my little pony. We get all kinds of terms this way though, like zipper, escalator, velcro, thermos, mesmorize, etc, so we can't just discount this use of the term. Language is evolving constantly! I think matchbox car, lego, and barbie are also going this way.
So...I have ambiguous feelings! I personally use "my little pony" a little differently depending on my audience. If I made a custom from a fakie base I would probably call it a "custom my little pony" to non-pony people, like my mom or my friends, so they would know what I was talking about without me having to enter some tedious description of cute plastic pony brand names, but I would call it a "custom fakie" here because it would not need the verbal shortcut of "my little pony". Actually I guess I should call it a "custom (fakie's brand name)" if I really wanted to be a stickler!