其实我觉得吧,两个句子在意义上没什么不同,大多情况可以混用
但是按照习惯,are you going表示的是很快就要发生的情况,比如：
-Oh,I'm sorry but I have to go home by now.
-OK,are you going by bus or on foot?
而will用在计划的时候比较好,比如：
-So Mary asked me to see her when the job's done.
-Really?Will you go by bus or on foot?