IMO the best way to go is a borosilicate glass bottle (handles frequent scrubbing and cleaning agents without problems) with a simple cap (no straw or sippy, mold/bacteria grows in there and it is impossible to clean out fully) a wide mouth (for easily getting a normal sized bottle brush inside) and with a fabric or rubber sleeve to avoid cracking when it inevitably gets bumped. Even then you'll need to occasionally check under the O-ring gasket in the cap for any bacterial growth; there's nothing like prying the gasket out and finding a couple of colonies of black mold staring back at you (ick) to ruin your day. Yes, it's heavy but most of us aren't using them in a situation where saving every gram counts.
Given the choice between glass or stainless steel, I'd still go with glass because it's easier to directly see dirty spots that you may have missed when scrubbing with the bottle brush and also because there's no risk of corrosion from bleach or other cleaning agents if bacteria/mold does start growing inside. If you're really thorough with cleaning and disciplined about doing it regularly, those might not be considerations.
[EDIT] I'd also give the nod to glass if you like flavorants with your water. I sometimes use a bit of lemon juice powder (not lemonade drink mix, that's something different; lemon juice powder is lemon juice that has been dehydrated with no additives) and stainless steel can develop corrosion pits from mildly acidic liquids over time.
I believe stainless steel has a slight anti-microbial property not present in glass.
Either way, both are far better than plastic. Plastic has no such anti-microbial effect AND tends to scratch from cleaning which makes wonderful footholds for bacteria. Further, because plastic is a hydrocarbon it is a potential food source for bacteria and fungus.
Even if the bacteria/fungus is harmless, you are looking at ingesting a bunch of plastic as it starts to degrade.
