Word from my-daughter-the-veterinarian:
I haven't worrried about this with [my dog] and he did drink out of plenty of lakes, but most of them are really high altitude. I kept him from drinking out of obviously yucky looking standing water though. It just depends how much lepto they see in your area, and how much risk you are willing to take (overall it's pretty small if you keep them out of ponds in cow pastures). It can come from other creatures besides elk urinating in the water (the organism is shed in the urine), but there may be a local issue up there with elk that I don't know about. The vaccine is not generally recommended as it causes some reactions occasionally and doesn't prevent the carrier/shedder state.
So you can filter or not--it's up to you and, of course, the water source. I know that I've increasingly been letting my Hysson drink out of streams, particularly in the high mountains. And since I may switch to a Steripen (I've just gotten one and am going to test out the battery life situation before deciding whether to keep or return it), in the interest of conserving batteries I may be doing a lot more of this.
Unfortunately most animals don't get referred to the UC Davis Vet Hospital until they're beyond the help of the neighborhood vet. By that time they're often beyond anyone's help!
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