@borkdude found this maybe-bug with SCI via Clerk… I built custom JS with this namespace:

(ns mathbox.clerk-ui
  (:require ["three" :as three]
            [nextjournal.clerk.sci-env]
            [sci.ctx-store]
            [sci.core :as sci]))

(def three-ns
  (-> (into {}
            (map (fn [[k v]] [(symbol k) v]))
            (.entries js/Object three))))

(sci.ctx-store/swap-ctx!
 sci/merge-opts
 {:namespaces  {'three three-ns}})

(js/console.log (new three/Color 0xff4136))