There was likely more than just Ned, Howland and Jon Snow.
There are clues and little tid-bits dropped here and there by George R. R. Martin, namely this recent interview:
[Interviewer] when Ned Stark and Howland Reed returned North from Dorne after the events at the Tower of Joy, etc. were they completely alone during that journey, or were they accompanied by some household guards, etc. for security?
[GRRM] You'll likely learn more about Ned's homecoming in future books. It's a long way from Dorne to Winterfell, a journey of months. More than that I'd rather not reveal just now.
So hang-tight, you will learn more.
The other deductions which we can do is the chronological events and likelyhoods, as follows:
1. Rhaegar and Lyanna disappear
2. Lyanna gets knocked-up
- At least nine months before the end of the War
- An unknown child is born, causing Lyanna to pass shortly after as a result of the child birth
- Rumoured to have been Jon Snow
- The real question is, how did she give birth with only 3 members of a Kingsguard (who were males and likely not versed in child-birth) present to help her?
- There's no way that The George would have relied on the timely arrival of Ned to help her
3. Showdown at the Tower of Joy
- Seven VS three skirmish known as the Showdown at the Tower of Joy occurs
- Combatants- Stark:
- Lord Ned Stark
- Lord Willem Dustin - perished
- Ser Mark Ryswell - perished
- Howland Reed (now Lord Howland Reed)
- Ethan Glover - perished
- Martyn Cassel - perished
- Theo Wull - perished
- Combatants - Targaryen:
- Lord Commander Gerold Hightower - perished
- Ser Oswell Whent - perished
- Ser Arthur "Sword of the Morning" Dayne - perished
4. Tower of Joy demolished
- This is where it gets strange
- An entire tower is demolished by two men?
- Ned and Howland remove stones from the tower and create 8 cairns for the dead combatants
5. The return home
- Ned and Howland make a small pit-stop at Starfall to return Dawn
- Lady Ashara Dayne (who was betrothed to Ned) throws herself from a tower, and commits suicide
- They stop over at King's Landing for some paper-work
- They continue on and bring Lyanna's bones, new baby (Jon Snow?) and all of their gear and supply home with them (excluding the bodies of the dead combatants)
- Somewhere along the journey, they pick up Wylla
- This would have to have been very early in the journey, or else Wylla was already with Lyanna in the Tower of Joy - there's no way that a newborn baby could have survived for so long without some sort of milk
As you can see, the details are hazy at best, and the only real details we have of the event is what Ned recollects in his "fever dream", which incidentally, GRRM says may not really be that accurate:
[Interviewer] what are the Kingsguards doing fighting Eddard? Eddard would never hurt Lyanna, nor her child. The little one would be safe with Eddard as well, him being a close relative. So I ask you, was there someone else with Lyanna and Jon?
[GRRM] You'll need to wait for future books to find out more about the Tower of Joy and what happened there, I fear.
I might mention, though, that Ned's account, which you refer to, was in the context of a dream... and a fever dream at that. Our dreams are not always literal.
My conclusion is that the most likely outcome was that Ned and co arrive at the ToJ, get into a punch-up and end up with only Ned, Howland and Lyanna (and perhaps a hand-maid or two).
Then, an unknown number of days or weeks pass and Lyanna gives birth. At this point, it's entirely possible that people have now joined this location. Another unknown amount of time passes (or doesn't) and Lyanna passes away.
Then, another unknown amount of time passes and Ned is found by "them" clutching her dead body. He may have spent a week or two mourning her death, cleaning up her body etc.
You see, now this fits both the canon of only Ned and Howland survived the skirmish, as well as "they" finding Ned clutching Lyanna's body.