Neither is pronounced th. In Modern Hebrew both are pronounced t. Th as in English through does not exist in native words. When it appears in loanwords, it is spelled ת' )the apostrophe is supposed to follow the ת( or (more correctly) ת׳.
In the same way that ב, כ and פ can represent both a hard sound and a soft sound (b/v, k/kh, p/f), ת used to represent both t and th, whereas ט represented an emphatic t.
Spelling of native Hebrew words is mostly based on etymology and tradition, not modern pronunciation.