Formal:
* Actually
* Certainly
* Truly
* Verily
* In fact
* As a matter of fact
* Without a doubt
* Absolutely
* Positively
* Definitely
Informal:
* Sure
* Really
* Honestly
* For sure
* Absolutely
* Definitely
* No doubt
Other options:
* In truth
* To be sure
* By all means
* Without question
The best synonym for "indeed" will depend on the specific situation and the desired tone.