What makes you think Nagisa's love for Rei is different from his love for Makoto and Haru?
Nice question! Nagisa is generally a very loving person and cares deeply about those around him, but I do think his love for Rei is a bit different (personally) because of the depth of his relationship with Rei. While he grew up with Haru and Makoto, his love for Rei was a sudden, strong attraction that developed into a deep relationship where his focus is nearly always concentrated on Rei, he constantly desires Rei’s attention and doting, and he is particuarly protective of Rei.
While Nagisa has always admired Haru and Makoto, his interest in Rei was sudden and so strong that he was relentless in his approach to Rei. He is overwhelmed with joy when Rei reciprocates his interest, too:
So it was very fast and strong, which suggests to me (albeit in a shipper lens) that there is a certain level of attraction involved on Nagisa’s part in these initial interactions, before he really knows Rei as a person.
Focused on Rei
As their friendship develops, Nagisa’s time, energy, attention span, gaze, thoughts, and jokes are all nearly directed at Rei. While it could be interpreted as a strong friendship, the kind of devoted attention he gives to Rei, as though he is unable to concentrate on anything else nor wants to, can be interpreted as romantic intrigue.
For better or for worse on Rei’s part, his attentions - kind, teasing, or otherwise - are directed almost entirely at Rei. This is why he is able to read Rei so easily at all times…
…is miserable when he doesn’t get attention back…
…and is almost always bickering with Rei in the background or spending any free moment around Rei.
And Nagisa loves attention from Rei, too, because he loves to get a rise out of him, one way or another, just to have that attention directed at him.
And he takes care of Rei more than anyone else…and relies on Rei more than anyone else
And, of course, this. Because Nagisa is so attentive to Rei, he is also more protective of and worried about Rei than anyone else. He always looks out for and checks in with his friends, wanting them all to get along, but Rei is arguably the only friend he is, on a second-to-second basis, making sure is 100% ok.
Not just jumping in front of him or taking the brunt of awkward situations…
…but also always checking in to make sure he is ok…
…and caring about his progress and feelings more than anyone else
And, of course, he depends on Rei, too, more than the others. He has a special need for Rei’s help, assurance, and protection as well. He relies on him in a different way than he does the other boys.
To keep him balanced
Out of trouble…
And for someone to study with, eat ice cream with, shoulder to sleep on, first person to call…etc. Their relationship is, undoubtedly, special and different, even if it’s not proven to be romantic.
And this is just a few things from the anime, let alone the incessant flirting in the drama CDs. Nagisa dressing as a girl to flirt with Rei…Nagisa going on a date with Rei to karaoke…falling asleep on Rei and dreaming about him…and always supporting and choosing Rei’s happiness, as seen in the mook…etc.