As written, the attack is made at disadvantage.
The most straightforward ruling here is that the attack is made with disadvantage. Manifest Echo states:
When you take the Attack action on your turn, any attack you make with that action can originate from your space or the echo's space. You make this choice for each attack.
You are still the one making an attack, so any conditions you have that influence attacks you make will also apply to an attack originating from the echo's space.
I have used a different ruling.
I have played as an Echo Knight as well as been the DM for an Echo Knight across two different campaigns, give some experience-based insight into using a different ruling than the one outlined above. In my games, I went with the ruling that attack's made from the echo's space are not at disadvantage, even if the real you is prone. First, there is a lore-based motivation for allowing this. From the description of the Echo Knight:
the Echo Knight has mastered the art of using dunamis to summon the fading shades of unrealized timelines to aid them in battle.
For me, the idea here is that despite having been knocked prone, there feasibly exists an unrealized timeline where you are not prone, and this is the one that is echoed.
Now, the main reason I advocate for this ruling is that it really doesn't unbalance anything, with one caveat. In the campaigns I ran/played, getting knocked prone didn't happen particularly often, and being able to offset the disadvantages of being prone with the echo was a good morale boost for the fighter in the moments that it happened.
The caveat: this ruling is prone to abuse if you let it work when the fighter goes prone intentionally. Notice that in the previous discussion, I was careful to specify "knocked prone". While prone, the following is true:
An attack roll against the creature has advantage if the attacker is within 5 feet of the creature. Otherwise, the attack roll has disadvantage.
As DM, when discussing this rule with the fighter, we went with something of a compromise: if you are knocked prone by a hostile creature's effect, attacks from the echo's space do not have disadvantage; if you drop prone yourself, attack's from the echo's space do have disadvantage. This was to prevent the fighter from intentionally dropping prone to give disadvantage to hostile ranged attackers while still being able to make ranged attacks without disadvantage. The narrative flavor I gave to this ruling was that if you drop prone on purpose, then all potential timelines proceeding from that one involved you being prone, so your echo is prone too.
Whatever ruling you go with, just be consistent. As I have noted elsewhere, the Echo Knight requires a bit of work, so be prepared to have many conversations with the DM about how to rule on this or that. I recommend keeping an extra sheet with your character sheet to keep track of the rulings you decide to go with, to help with maintaining consistency across the campaign.