A great deal depends on the stress. If thought receives strong stress, then it really doesn't matter which one you say; they'll come out the same anyway.
The consonant cluster /dθ/ is very hard for English speakers to pronounce, and we tend to elide it to simply /θ/, which would delete the only mark of the past perfect auxiliary had, and make the two forms indistinguishable in ordinary speech.
- I had thought ... would come out /ayd 'θɔt .../; /dθ/ => /θ/, producing */ay 'θɔt .../
- I thought ... would come out /ay 'θɔt .../, the same as the other one.
How you write it is up to you. Grammar is about spoken language, not writing.