To be CLEAR - your question is about staying at the Hotel Old Quarter which also has a bar in its main level? I think I'd choose slightly more off-the-beaten-path for bars, restaurants, and hotel, but some folks really like that energy.
From a location perspective, the HOQ definitely is down there near a lot of the tourist traffic. I personally prefer to stay a bit further "out" towards the main canals or, most recently, out in Leidseplein closer to the Vondelpark. I think Jordaan would be lovely, and both are better for getting to something like the Anne Frank House (Jordaan is right there, and walking down a canal like the Prinsengracht from Leidsenplein to the AFH is nice).
In Amsterdam, pre-WWI, there was a vibrant Jewish community (Jodenbuurt). In WWII, of course, the Nazis took advantage of that situation and greatly restricted Jewish rights and movement (and eventually full on persecution & deportation to concentration camps), and now the area has a mixture of Jewish history, Holocaust related history, and synagogues & other culturally significant places.
Perhaps fulfilling your "quirky and comfy" option, the Banks Mansion Hotel would work - closer to the the Jewish area, but also out of the busier touristy area (but tourism is every where in Amsterdam).