The issue of hours of work is a complicated one, and usually something that is better resolved by compromise than by insisting on a 'no exceptions' approach to following 'the rules'.
I've regularly been in environments where there has been a tension between 'creative' people who feel free to work the hours they suit, justifying their arriving 'late' by the fact they work very many more hours than eight in total each day, and perhaps even more days a week than five.
If this is your only issue with your co-founder, perhaps you need to revise your own expectations. You describe the guy as lazy, but it seems that the laziness is only in the form of coming late. He still seems to work 40+ hours a week, and you don't indicate any unhappiness with his outputs.
Realistically, most companies with developers choose to take a somewhat relaxed approach to hours of work. They'd rather have happy developers who productively work 50+ hours a week at unusual hours of the day and night, than to have unhappy developers who 'punch the clock' between 9am and 5pm each day and no more than that.
On the other hand, it is fair to suggest there be predictable 'core hours' of work where everyone knows everyone will be at work and available.
As for degrading the morale, it seems your office has three people only in it? You, your partner, and the intern. My gentle suggestion here is that it is you who is degrading the morale, not your partner. If you accept with positive good grace your partner's working hours, and if you convey this to the intern, then neither you nor the intern need to feel negative any further.
One more thing - if this person is indeed your equal partner, you can't unilaterally choose/dictate to him what he does. Maybe, if we look carefully through Founder Dating, we might find him posting 'Help, my partner is obsessing over my hours of work and refuses to acknowledge I'm contributing more than my fair share, while all she does is complain about what time I get into the office each morning'!
Sorry not to be totally sympathetic to your plight, but sometimes we have to change ourselves, particularly when we can't change those around us.