A few things to consider:
1) Will it be you and your kids, or will you have other adults along with you? The more adults to help with toddlers, the easier it is to stay at a non-boat-to-MK or monorail resort.
2) Where do you plan to spend your time? If you think your visit will be MK heavy, then I'd stay at WL (even though I personally prefer POFQ). The boat to MK with two very young kids is much easier than the bus, especially if it's just you and kids (per my question above...the bus is gets easier with more adult plus kids, but if you're at MK all the time, WL makes the most sense).
3) If you'll be at other parks or plan to spend time at the pool, I'd consider POFQ. They have a great pool and splash area for little kids.
4) With such little kids, QS might be fine for your needs. I'd have a hard time not having a TS meal during my trip, but that's me.
I'm not a huge fan of WL just because the theme doesn't appeal to me. But it has great amenities and is a very quick boat ride to MK. With such little kids, I'd *probably* choose WL and pay out of pocket for any TS meals I'd have....but it would be a difficult decision for me.