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Which is better for a counter assault unit?

A chapter master with a honour guard

Or

A captain with a cc oriented command squad?

And should each different unit be outfitted?

Standard caveat: TH/SS termies will beat both these units in terms of bang for the buck.

Honor Guard Pros:
2+ save is better now
They come with power weapons standard (and can be outfitted with a mix of swords and axes for speed and hitting power)
Can take Chapter Standard for 4 attacks per model

Command Squad Pros:
Captain is better than Chapter Master (fewer points for basically the same unit)
Apothecary gives FNP
Can take SS for durability vs. power weapons
Can take a mix of strong CC wargear, but it adds up quickly

Honestly, it's a bit of a wash, assuming you're at all concerned with cost-effectiveness. Neither unit will stand up to a real 6e deathstar with durability and AP2 CC weaponry, that's what TH/SS termies are for. On the other hand, against something in their own weight class they'll both acquit themselves well. Honor Guard will be less threatened by a certain class of formerly dangerous units (essentially, any unit with AP3 CC weaponry) and come pre-loaded with power weapons as well as the cool factor, so they get my vote. By the time you give everyone in the Command squad the appropriate weaponry, the cost is pretty comparable.

So just take some termies instead?

And would regular termies or tactical termies do better in gunline army?

Tactical are regular termies. Hammernators or Termy assault squad can have lightning claws or hammers and shields.

Always go with AT LEAST 2-3 hammer/shield guys, just because it's so cheap and you'll never find yourself without a way to kill that pesky MC or deathstar.

And, you can soak lascannons.

Marshall Ragnar wrote:So just take some termies instead?

And would regular termies or tactical termies do better in gunline army?

If you're looking for the "best" counterassault choice for your army, then yes, take TH/SS assault terminators instead. There's really no competition from an effectiveness standpoint. Honor Guard are cool, though, and I'm interested to see how they do under the new rules. My local meta is very laid back, so I'm able to run fluffy lists and test out the units I like.

Also, Honor Guard can be used with Marneus "Call Me Daddy" Calgar. He's a lot more badass under 6e rules, now that most of his big competition (Draigo, Abbadon, Mephiston, etc.) is AP3 in CC.

The problem with the comparison to Termies is cost-effectiveness for the role. It's an awful lot of points to tie up in the HG/CS for a counter-assault unit unless it's your only assault unit in an otherwise shooty list. Otherwise, splashing out on a fully equipped HQ and bodyguard is too much of a premium.
I could see this being partly viable if you split the HQ off separately to help your force elsewhere, but the TH/SS Termies are still more durable and therefore better to tie units up.

If you plan to use such a unit in a proper assault role, however, it's absolutely worth taking the HG/CS. They have more of a place against lighter, more numerous foes than TH/SS Termies, as they can put out more attacks thanks to extra weapons AND strike first on most occasions too. If you're going this route, you want a good mix of options in the unit - at least one axe/fist if not two.
Which one you take would depend on your opponent. The HG are more killy but more fragile to pay for it, so it depends largely what kind of AP weaponry you're up against.

Honour guard used to be a curve ball choice but were interesting choice when you could charge from razorbacks, for the counterassault role you describe.

However, now they need a raider to get them into the action, in which case go the whole hog and get the assault termies.

Command squads are nice for cc, in the sense that they can land in a drop pod with 4 plasma guns, then fight back when they get assaulted.

Also command squad on bikes I am particularly enjoying I must say. Apart from getting a little too close to a vindicator, they are doing very well indeed though you would expect so for the points.