Recommended if you prioritize: access from JR Akihabara Station and modern style
The lowest room rate for 2: 120-230 USD
Remm Akihabara is located just one minute away from JR Akihabara Station. The hotel had a renovation on the top floors, so you could choose those if you prefer a nice new room. A cool thing about this hotel is that the room on the 'Lady's Floor' offers skincare amenities designated for female. Also, all rooms have massage chair for you to relax from a long day.
Recommended if you prioritize: onsen and transportation access
The lowest room rate for 2: 80 - 200 USD
Dormy Inn is one of the popular business hotel brand. One of the highlight of this hotel is that it has access to 6 stations within 5-minute walking distance. This will be very handy when you are traveling to different sites. Also, they have a great onsen for you to release your fatigue.
It is a premium brand of Dormy group but it still is a business hotel so the room is not that big.
Recommended if you prioritize: ryokan feeling and onsen
The lowest room rate for 2: 110~ USD
Ochanomizu Shoryukan is actually one station away from Akihabara, located 5 minutes away from JR Ochanomizu Station. If you want to stay at ryokan feeling hotel without going outside of Tokyo, this is your choice. It offers modern traditional rooms and big public onsen. If you hasitate to take a bath with someone else, book a room with onsen.