Before I answer, I'm not sure that you understand what a spell is, so I'm going to cover that first. My apologies if you know.
A spell is a card on a stack, which is to say a card that has been cast but hasn't yet resolved, hasn't been countered and hasn't otherwise left the stack.
e.g. If you cast Llanowar Elves, it is a spell from the time you take it out of your hand until it enters the battlefield.
e.g. If you cast Giant Growth, it is a spell from the time you take it out of your hand until it resolves to give a +3/+3 bonus to a creature.
A continuous effect is not a spell.
e.g. The +3/+3 granted by Giant Growth is not a spell.
Cards on the battlefield are not spells.
e.g. An artifact attached to a creature is not spell.
Now on to the questions.
If they boosts their creature with a +3/+3 spell, can you counter the spell?
Depends on the spell you used to counter.
If they boost their creature with an equipment card, during his combat attack phase, can you counter that?
It's not clear what you mean.
If they are casting an Equipment spell, you can counter that. They wouldn't normally be allowed to do cast an Equipment spell in the Combat Phase, though.
If they are using the Equip ability Equipment, you can counter that, there are a very few cards (e.g. Stifle) that can do it. They wouldn't normally be allowed to use Equip in the Combat Phase, though.
If they are attaching the Equipment using an ability other than Equip (e.g. Brass Squire's), Stifle would do the trick again.
Keep in mind that you can't counter permanents (objects on the battlefield) and the effects of their static abilities (e.g. Bladed Bracers's +1/+1), just abilities on the stack and spells.