Yes, the high and low states are reversed, if you put a high in you get a low out and vice versa. The actual voltages don't have to be as high as 4.8V or as low as 0.04V, the threshold is somewhere in the 2.4V region so as long as you are significantly above or below that voltage you should be OK. I suggested the 7406 because it has "open collector" outputs, in other words the output isn't driven high from inside the IC, you have to pull each output high with a resistor to +5V outside the IC. My reasoning was that it lets you safely short the output to ground without risk of damage, if the dip switches are not connected directly to an IC output pin, you can use the 7404 IC instead which has outputs which are driven high as well as low from inside the chip.
Sounds like your eraser isn't up to the job. It's a pity we are so far apart because I have tubes of 27C64s here which will probably never be used and you would be welcome to have them. Before buying new ones though, try something: Clean the windows of the EPROMs with a solvent, alcohol or similar should work, then put them in the eraser for about 20 minutes. Then rotate them 180 degrees and give them a further 20 minutes before trying them again. Each cell on the chip surface is extremely tiny and even a minute speck of dirt on the window will cast a large shadow on the cells. Changing their orientation will help to irradiate them from a different angle. There is another trick which I have never tried but I'm assured works on 'tired' EPROMs, ones that refuse to erase or reprogram, you bake them in an oven for about an hour at around 150C. It's not hot enough to melt the package or solder but enough to make the silcon conductive and therefore leak away any charge left in the cells. I would use it as a last resort but it might be worth a go.
Brian.