CLS's LRAP will cover PI work even if you enter it after you've clerked. There is no cap on how much they'll pay back. So, even if you go entirely on loans for all three years, they'll pay it all back for you. The income threshold is $50k. Above $50k, they'll still pay back loans for you, but you'll have to pay 37.5% of your income above that. For instance, if your PI job pays $60k, then you will owe $3,750 (37.5% of the 10k above 50k) toward your loan payments for the year. CLS will pick up the rest.
If you get one of CLS's PI fellowships, they raise the income threshold to $100k. At that income level, you can be guaranteed you'll never owe a dime. Well, that, or you have the ballinest PI job ever.
I know nothing about how Boalt or HLS LRAPs work, but I know the CLS one well. It is quite generous and has been known to allow a person to qualify even if they work at a firm, provided they do certain kinds of work at the firm.
Also, the Dean just held a meeting where he told us that Columbia is changing it to allow people to combine it with the federal government's LRAP program for an even better pay back. If you are sure PI is where you want to be, this new combination plan looks killer.
Any one of these schools will get you a PI job anywhere in the country you want to go. Obviously, some jobs are more prestigious than others and will require better grades. The higher up the chain you go, the more latitude you have to mess up. So, HLS might give you more wiggle room than CLS which will give you more wiggle room than Boalt. But, the wiggle room you have won't be much from school to school. Go where you'll be happiest. If that's where you know you'll come out owing the least, pick CLS. If that's where you'll be closest to your SO, then pick Boalt. I can't think of a good reason to pick HLS, except that it IS HLS. Of course, some will say that's a reason NOT to choose it.