Yogyakarta's probably 40 miles or so closer (which in terms of Indonesian roads may potentially be longer than you may think).
The "problem" with Yogyakarta is that your only nonstop option from Singapore is AirAsia, so if you're expecting business class comforts then it's not the right choice for you! Having said that, the one and only time I've flown AirAsia* I thought it was fine for a short trip but I certainly wouldn't want to fly them for anything more than a couple of hours.
(*I was in Jakarta for business and was joining some friends for a weekend in Bali, and was specifically told by Indonesian contacts that the safer airlines to fly domestically were Garuda and AirAsia, and the latter ended up cheaper)