Are any of these options preferred, or is there an even better option/technique out there?

Photography is all about tradeoffs. You can compensate for low light by using a longer exposure, or increasing the aperture, or increasing the sensitivity (ISO), or adding more light. You can reduce noise by using lower sensitivity, or decreasing the exposure time, or stacking several images, or buying a camera with better low light performance. All these options are legitimate, but each one comes with some sort of cost, and how you choose to balance the various parameters is really up to you.

One thing you don't seem to have considered is just shooting with more ambient light. I expect that you're mostly interested in making images that look like they were created in dim surroundings and that you aren't necessarily wedded to the experience of shooting in the dark. If you increase the ambient light by a factor of 4 and drop the ISO 2 stops, you'll get the same exposure but less noise. This is a case of using photography's tradeoffs to your advantage: you can create a very low light look even when you've got more than enough light to get a noise-free image.

Before you say get a flash, I like the natural look you get from just the ambient light and even if I used a nice flash that's well diffused I can still tell that a flash was used.

Aside from intensity and duration, there's no actual difference between ambient light and flash... it's all just light. Take a look at the Lighting 101 lessons at strobist.com to begin to learn about how to move your flash off camera, and how to control the shape, color, and intensity so that your photos don't have that recognizable flash look.