I really liked The House in the Cerulean Sea. I've had the sequel--Somewhere Beyond the Sea--on my TBR for a while now, but after reading In the Lives of Puppets last year, the sequel got pushed further down my list. Puppets isn't good. My next LGBT book is: The Sweetness of Water. It's for book club in February.
For what it's worth, the Stranger Things book I was talking about above, "Rebel Robin," is very much an LGBT book as well, since much of it is about Robin gradually accepting that, yeah, she likes girls.
Our local library even put a rainbow sticker on the spine, identifying it as LGBT-themed.