IMO C
Correct idiom is estimate to be but option E has other issues.
I guess E compare or contrast two estimations : one by Interstudy and other by the HOM's themselves.

(A) they estimate that, in comparison to last year, when only 36 percent of the nation's 607 HMO's was profitable, this year 73 percent will be (they doesn't agree with singular subject Interstudy)
(B) compared to only 36 percent of the nation's 607 HMO's being profitable last year, they estimate 73 percent would be this year (comma splice)
(C) only 36 percent of the nation's 607 HMO's were profitable last year; it estimates that this year 73 percent will be (Contender answer choice .I guess this year 73 percent will be sounds awkward though )
(D) it estimates 73 percent of the nation's 607 HMO's would be profitable this year; last year that was only 36 percent (that doesn't have proper referent)
(E) only 36 percent of the nation's 607 HMO's last year were profitable, whereas they estimate it this year to be 73 percent (they can only refer to HMO's here..I doubt what "it" refers to)

whats the OA and the source?

OA: C

According to Interstudy, a nonprofit organization that studies health maintenance organizations (HMO's), they estimate that, in comparison to last year, when only 36 percent of the nation's 607 HMO's was profitable, this year 73 percent will be.

(A) they estimate that, in comparison to last year, when only 36 percent of the nation's 607 HMO's was profitable, this year 73 percent will be -> they is ambigous
(B) compared to only 36 percent of the nation's 607 HMO's being profitable last year, they estimate 73 percent would be this year -> they is ambigous
(C) only 36 percent of the nation's 607 HMO's were profitable last year; it estimates that this year 73 percent will be
(D) it estimates 73 percent of the nation's 607 HMO's would be profitable this year; last year that was only 36 percent -> that usage is ambigous
(E) only 36 percent of the nation's 607 HMO's last year were profitable, whereas they estimate it this year to be 73 percent -> they is ambigous

IMO C

Remove the modifier.. "a nonprofit organization that studies health maintenance organization" and you will see that only C and E make sense.. E is run-on .. so we are left with C. Also, E has pronoun error.. 'they' should be 'it' refer to correctly refer to Interstudy.

Hope this helps.