Before I start, let me tell you that there is no hotels right by either stations.  I will list the ones that I know is good but there is a bit of a walk. 

1. Dormny Inn Premium SHibuya Jingumae

Recommended if you prioritize: onsen

The lowest room rate for 2: 230USD~

Dormny Inn Premium SHibuya Jingumae is a premium brand hotel of business hotel group, Dormy Inn.  The highlight of this hotel is for sure the onsen.  They use super soft water which is good for your skin and skin.  This is actually the closest hotel to a Station in Harajuku (Meijijingumae Station) but still 6 minutes far by walk.  If it is too far for you, choose a hotel near Shibuya Station and hop on the train to go to Harajuku and Omotesando area.

2. Hotel Allamanda Aoyama

Recommended if you prioritize: the access to Omotesando and Aoyama

The lowest room rate for 2: 280 USD~

This hotel has a member's only fitness and spa club inside of the building and hotel residences get a free access, which is pretty cool for this price.  The room is definitely bigger than business hotels.  The hotel is located right in front of Ginza line Gaienmae station, so you have to travel one station to get to Omotesando.