Both are wrong. If you want to say *why don't we go to school?*, you just say, 学校へ行きませんか？？or 学校に行きませんか？ If you want to say* why you don't go to school?*, どうして(あなたは)学校に行かないのですか？

Both of へ and に are appropriate on this context, but 行きませんか is not. Replace 行きませんか with 行かないのですか. どうして学校 {へ , に} 行かないのですか。

@mari "学校に行きませんか？" I remember this means you invite someone to go to school together, is it right? Then this translation is quite different from the meaning of "why don't we go to school ?".

2. Place + " に"