Gluten AND Dairy Free in SOHO
I can't speak to the dairy free side of things, but I've eaten gluten free successfully at a number of places in Soho. Like sgordon mentioned, Bread is a surprisingly safe bet, and they even have gluten-free pasta available. Rubirosa also has an extensive gluten-free menu, and it looks like they have some items that are or could probably be made dairy-free as well. I also had a great meal recently at Jack's Wife Freda on Lafayette, and they were really accommodating. The peri peri chicken is really good.
Butcher's Daughter - a "mostly vegan" (they occasionally use eggs, but no dairy) place that recently opened could be a good option. Lots of salads and such, and I noticed a "linguini" made of squash on the menu. I think the most expensive item on the menu is, like, $16. More of a snack / lunch place than a meal place.
Not far from SoHo is Chinatown, and there are lots of options there - there's no dairy in Chinese cuisine, for the most part. As to the gluten - I'll ask if your sister's restriction is due to Celiac's or if it's just the latest gluten-free fad diet. If it's the former, how sensitive she is to cross-contamination and such.
Mexican places can work, as most of the grains are going to be corn and/or rice. Just don't order anything with cheese on it, and stick to corn tortillas for those items that come wrapped. La Esquina is good (there's a taco stand, a casual restaurant around the corner, and a fancier restaurant in the basement) - for something rootsier Cafe El Portal is a fun little place. Mexican Radio is also okay for nothing fancy, something to go with a margarita or two. Cafe Habana - which is Cuban, not Mexican, obviously - probably has a number of options as well. Good lunch spot, but crazy busy on the weekends.
Blue Ribbon Brasserie has a very extensive menu - a real something-for-everyone place. And very solid food. More of a nice night out place, if not a super-fancy one.
Bread on Spring St. (though you wouldn't think it from the name) probably has a number of things - lots of salads and such on the menu.
There's a new Vegan place called Rawlicious on Centre St - never been, but I suspect they'd have a few options.
There are a number of good little salads, spanish omelettes, and snacky tapas things at Despana on Broome. Great little place.
Cocoron on Kenmare does buckwheat (which isn't actually wheat and conatins no gluten) soba, though i'd check with them if it's 100% buckwheat first. They're really good, though.